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      Systematic analysis of 1298 RNA‐Seq samples and construction of a comprehensive soybean ( Glycine max ) expression atlas

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          Abstract

          <p class="first" id="d8068036e107">Soybean (Glycine max [L.] Merr.) is a major crop in animal feed and human nutrition, mainly for its rich protein and oil contents. The remarkable rise in soybean transcriptome studies over the past 5 years generated an enormous amount of RNA-seq data, encompassing various tissues, developmental conditions and genotypes. In this study, we have collected data from 1298 publicly available soybean transcriptome samples, processed the raw sequencing reads and mapped them to the soybean reference genome in a systematic fashion. We found that 94% of the annotated genes (52 737/56 044) had detectable expression in at least one sample. Unsupervised clustering revealed three major groups, comprising samples from aerial, underground and seed/seed-related parts. We found 452 genes with uniform and constant expression levels, supporting their roles as housekeeping genes. On the other hand, 1349 genes showed heavily biased expression patterns towards particular tissues. A transcript-level analysis revealed that 95% (70 963 of 74 490) of the assembled transcripts have intron chains exactly matching those from known transcripts, whereas 3256 assembled transcripts represent potentially novel splicing isoforms. The dataset compiled here constitute a new resource for the community, which can be downloaded or accessed through a user-friendly web interface at http://venanciogroup.uenf.br/resources/. This comprehensive transcriptome atlas will likely accelerate research on soybean genetics and genomics. </p>

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          Author and article information

          Contributors
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          Journal
          The Plant Journal
          Plant J
          Wiley
          0960-7412
          1365-313X
          August 2020
          August 13 2020
          August 2020
          : 103
          : 5
          : 1894-1909
          Affiliations
          [1 ]Laboratório de Química e Função de Proteínas e Peptídeos Centro de Biociências e Biotecnologia Universidade Estadual do Norte Fluminense Darcy Ribeiro Campos dos Goytacazes Brazil
          Article
          10.1111/tpj.14850
          32445587
          06456815-53ca-44c8-bc33-f79eda934b38
          © 2020

          http://onlinelibrary.wiley.com/termsAndConditions#vor

          http://doi.wiley.com/10.1002/tdm_license_1.1

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